A data storage device is disclosed comprising a head actuated over a disk comprising a plurality of data tracks. A plurality of access commands including a plurality of write commands are stored in a command queue, and the access commands are sorted into an execution order. A first write command is selected from the command queue based on the execution order, and a first part of the first write command is executed leaving a runt write command. The runt write command is executed between two of the sorted access commands so that the runt write command does not affect the execution order.